Methods to Improve Our Understanding of the Health and Welfare Status of Sheep (Ovis Aries) and the Influences of their Immediate Environment

Studies into the effective use of accelerometers in the automated assessment of sheep behaviour to improve welfare has increased exponentially with promising preliminary results. Previous research has focused primarily on explicit behaviour classification, for example, parturition and urination events, with a view to create a commercial tool that will provide health warnings for farmers. Yet the majority of trials have not been conducted in a farm environment. This study aims to provide essential primary research investigating environmental variables that may influence the behavioural patterns of a commercial flock. This vital information has been largely overlooked and crucial when considering tools that provide health warnings, due to the many factors that influence sheep behaviour such as weather, vegetation, soil type, land typography and breed (Hinch, 2017). The primary aim of this study was to assess the most appropriate model to predict the behaviours of commercial ewes. This was achieved by deploying accelerometers on a commercial flock and simultaneously collecting manual observations and video recordings of flock’s individual activity. The raw acceleration data was processed to create 6 variables. Behaviour classification was also evaluated using three ethograms, each with two mutually exclusive behavioural/postural states: 1. Head Position (head up/down), 2. Posture (standing/lying), 3. Activity (resting/grazing). Three Window setting (3, 5 and 7 seconds) and five machine learning algorithms 4 (Linear Discriminate Analysis (LDA), Classification and Regression Trees (CART), K Nearest Neighbour (KNN), Support Vector Machines (SVM) and Random Forest (RF)) were evaluated. Results indicated a RF with a 7 second window the optimal model across all ethograms. (Accuracy by ethogram; 1) 91.5%, 2) 91.0% and 3) 99.3%). The secondary aim of this study was to use a Linear Mixed Model (LMM) to investigate the influence of temperature and rainfall on grazing and resting behaviours. This was accomplished by using the initially developed model (RF) on data collected from an unsupervised commercial flock, recorded in a second trial. Results indicated that there was a significant positive relationship between grazing durations and rainfall (p.001), this finding conflicts with previous research observations and is yet unpublished. In addition, prior sheep behaviour research has suggested ‘foraging’ as the dominant activity, results from this trial indicate the dominant daily activity was resting (67% of daily activity). In conclusion this study highlights the difficultly of defining what ‘normal’ sheep behaviour is and that it is not viable to implement a ‘one-size fits all’ approach. Further research is required in the behavioural assessment for this particularly malleable species

Establishing best practice for the classification of shark behaviour from bio-logging data

Understanding the behaviours of free-ranging animals over biologically meaningful time scales (e.g. diel, tidal, lunar, seasonal, annual) gives important insights into their ecology. Bio-logging tools allow the remote study of elusive or inaccessible animals by recording high resolution multi-channel movement data, however archival device recording duration is limited to relatively short temporal-scales by memory and battery capacity. Machine learning (ML) is becoming common for automatic classification of behaviours from large data sets. This thesis develops a framework for the programming of bio-loggers for the classification of shark behaviour through the optimisation of sampling frequency (Chapter 2) and the choice of movement sensor (Chapter 3). The effects of sampling frequency on behavioural classification were assessed using data published in a previous study collected from accelerometer equipped juvenile lemon sharks (Negaprion brevirostris) during captive trials in Bimini, Bahamas. The impacts of different combinations of movement sensors (accelerometer, magnetometer and gyroscope) were assessed using data collected from sub adult sicklefin lemon sharks (Negaprion acutidens). Sharks were equipped with multi-sensor devices recording acceleration, angular rotation and angular velocity during captive trials at St Joseph Atoll, Seychelles. Catalogues of discrete classes of behaviours (ethograms) were developed by observing sharks during captive trials. Behaviours (swim, rest, burst, chafe, headshake) were classified using a random forest ML algorithm with predictor variables extracted from the ground-truthed data. A range of sampling frequencies (30, 15, 10, 5, 3 and 1 Hz) and combinations of movement sensors were tested. For each dataset, a confusion matrix was determined from model predictions for calculation and comparison of evaluation metrics. Classifier performance was best described by the class or macro F- score, a measure of model performance, one indicating perfect classification and zero indicating no classification. As sampling frequency decreased, classifier performance decreased. Best overall classification was achieved at 30 Hz (F- score >0.790), although 5 Hz was appropriate for classification of swim and rest (>0.964). Behaviours characterised by complex movements (headshake, burst, chafe) were best classified at 30 Hz (0.535- 0.846). Classification of behaviours was best with a tri-sensor combination (0.597), although incorporating an additional sensor (magnetometer or gyroscope) resulted in little increase in classifier performance compared to using an accelerometer alone (0.590 compared to 0.535 respectively). These results demonstrate the ideal sampling frequencies and movement sensors for best-practice programming of bio-logging devices for classifying shark behaviour over extended durations. This thesis will inform future studies incorporating behaviour classification, enabling improved classifier performance and extending recording duration of bio-logging devices

Rumination Detection in Sheep: A Systematic Review of Sensor-Based Approaches

The use of sensors to analyze behavior in sheep has gained increasing attention in scientific research. This systematic review aims to provide an overview of the sensors developed and used to detect rumination behavior in sheep in scientific research. Moreover, this overview provides details of the sensors that are currently commercially available and describes their suitability for sheep based on the information provided in the literature found. Furthermore, this overview lists the best sensor performances in terms of achieved accuracy, sensitivity, precision, and specificity in rumination detection, detailing, when applicable, the sensor position and epoch settings that were used to achieve the best results. Challenges and areas for future research and development are also identified. A search strategy was implemented in the databases PubMed, Web of Science, and Livivo, yielding a total of 935 articles. After reviewing the summaries of 57 articles remaining following filtration (exclusion) of repeated and unsuitable articles, 17 articles fully met the pre-established criteria (peer-reviewed; published between 2012 and 2023 in English or German; with a particular focus on sensors detecting rumination in sheep) and were included in this review. The guidelines outlined in the PRISMA 2020 methodology were followed. The results indicate that sensor-based systems have been utilized to monitor and analyze rumination behavior, among other behaviors. Notably, none of the sensors identified in this review were specifically designed for sheep. In order to meet the specific needs of sheep, a customized sensor solution is necessary. Additionally, further investigation of the optimal sensor position and epoch settings is necessary. Implications: The utilization of such sensors has significant implications for improving sheep welfare and enhancing our knowledge of their behavior in various contexts

Prying into the intimate secrets of animal lives; software beyond hardware for comprehensive annotation in ‘Daily Diary’ tags

Smart tags attached to freely-roaming animals recording multiple parameters at infra-second rates are becoming commonplace, and are transforming our understanding of the way wild animals operate. However, interpretation of such data is complex and currently limits the ability of biologists to realise the value of their recorded information. This work presents a single program, FRAMEWORK 4, that uses a particular sensor constellation described in the?Daily Diary? tag (recording tri-axial acceleration, tri-axial magnetic field intensity, pressure and e.g. temperature and light intensity) to determine the 4 key elements considered pivotal within the conception of the tag. These are; animal trajectory, behaviour, energy expenditure and quantification of the environment in which the animal operates. The program takes the original data recorded by the Daily Dairy and transforms it into dead-reckoned movements,template-matched behaviours, dynamic body acceleration-derived energetics and positionlinked environmental data before outputting it all into a single file. Biologists are thus left with a single data set where animal actions and environmental conditions can be linked across time and space.Fil: Walker, James S.. Swansea University. College Of Sciences; Reino UnidoFil: Jones, Mark W.. Swansea University. College Of Sciences; Reino UnidoFil: Laramee, Robert S.. Swansea University. College Of Sciences; Reino UnidoFil: Holton, Mark D.. Swansea University; Reino UnidoFil: Shepard, Emily L. C.. Swansea University. College Of Sciences; Reino UnidoFil: Williams, Hannah J.. Swansea University. College Of Sciences; Reino UnidoFil: Scantlebury, D. Michael. The Queens University Of Belfast; IrlandaFil: Marks, Nikki, J.. The Queens University Of Belfast; IrlandaFil: Magowan, Elizabeth A.. The Queens University Of Belfast; IrlandaFil: Maguire, Iain E.. The Queens University Of Belfast; IrlandaFil: Grundy, Ed. Swansea University. College Of Sciences; Reino UnidoFil: Di Virgilio, Agustina Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Patagonia Norte. Instituto de Investigación En Biodiversidad y Medioambiente; Argentina. Universidad Nacional del Comahue; ArgentinaFil: Wilson, Rory P.. Swansea University. College Of Sciences; Reino Unid

Quantifying allo-grooming in wild chacma baboons (Papio ursinus) using tri-axial acceleration data and machine learning

Quantification of activity budgets is pivotal for understanding how animals respond to changes in their environment. Social grooming is a key activity that underpins various social processes with consequences for health and fitness. Traditional methods use direct (focal) observations to calculate grooming rates, providing systematic but sparse data. Accelerometers, in contrast, can quantify activity budgets continuously but have not been used to quantify social grooming. We test whether grooming can be accurately identified using machine learning (random forest model) trained on labelled acceleration data from wild chacma baboons (Papio ursinus). We successfully identified giving and receiving grooming with high precision (81% and 91%) and recall (87% and 79%). Giving grooming was associated with a distinct rhythmical signal along the surge axis. Receiving grooming had similar acceleration signals to resting, and thus was more difficult to assign. We applied our machine learning model to n = 680 collar data days from n = 12 baboons and found that grooming rates obtained from accelerometers were significantly and positively correlated with direct observation rates for giving but not receiving grooming. The ability to collect continuous grooming data in wild populations will allow researchers to re-examine and expand upon long-standing questions regarding the formation and function of grooming bonds

Assessing the utility and limitations of accelerometers and machine learning approaches in classifying behaviour during lactation in a phocid seal

Background Classifying behaviour with animal-borne accelerometers is quickly becoming a popular tool for remotely observing behavioural states in a variety of species. Most accelerometry work in pinnipeds has focused on classifying behaviour at sea often quantifying behavioural trade-offs associated with foraging and diving in income breeders. Very little work to date has been done to resolve behaviour during the critical period of lactation in a capital breeder. Capital breeding phocids possess finite reserves that they must allocate appropriately to maintain themselves and their new offspring during their brief nursing period. Within this short time, fine-scale behavioural trade-offs can have significant fitness consequences for mother and offspring and must be carefully managed. Here, we present a case study in extracting and classifying lactation behaviours in a wild, breeding pinniped, the grey seal (Halichoerus grypus). Results Using random forest models, we were able to resolve 4 behavioural states that constitute the majority of a female grey seals’ activity budget during lactation. Resting, alert, nursing, and a form of pup interaction were extracted and classified reliably. For the first time, we quantified the potential confounding variance associated with individual differences in a wild context as well as differences due to sampling location in a largely inactive model species. Conclusions At this stage, the majority of a female grey seal’s activity budget was classified well using accelerometers, but some rare and context-dependent behaviours were not well captured. While we did find significant variation between individuals in behavioural mechanics, individuals did not differ significantly within themselves; inter-individual variability should be an important consideration in future efforts. These methods can be extended to other efforts to study grey seals and other pinnipeds who exhibit a capital breeding system. Using accelerometers to classify behaviour during lactation allows for fine-scale assessments of time and energy trade-offs for species with fixed stores

Classifying the posture and activity of ewes and lambs using accelerometers and machine learning on a commercial flock

This is the final version. Available on open access from Elsevier via the DOI in this recordData Availability: A censored version of the data is available upon request.Early decision making in commercial livestock systems is key to maximising animal welfare and production. Detailed information on an animal’s phenotype is needed to facilitate this, but can be difficult to obtain in a commercial setting. Research into the use of bio-logging on sheep to continuously monitor individual behaviour and indirectly inform health and production has seen rapid growth in recent years. Much of this research, however, has been conducted on small numbers of animals in an experimental setting and over limited time periods. Previous studies have also focused on ewes and there has been little research on the potential of bio-logging for collecting behavioural data on lambs, despite clear potential relevance for production. The present study aimed to test the feasibility of deploying accelerometers on a commercial sheep flock at a key point in the annual production cycle (lambing), to validate the viability of automated monitoring of sheep behaviour in a commercial setting. Also, we aimed to develop robust machine learning algorithms that can classify both the posture and physical activity of adult sheep and lambs. We used a Random Forest machine learning algorithm to predict: two mutually exclusive postures in ewes and lambs (standing and lying), achieving average accuracies of 83.7% and 85.9% respectively; four mutually exclusive activities in ewes (grazing, ruminating, inactive and walking), achieving an average accuracy of 70.9%; and three mutually exclusive activities in lambs (inactive, suckling, walking), achieving an average accuracy of 80.8%. These performance accuracies on large numbers of individuals afford the opportunity to provide a detailed understanding of the daily activity budget of ewes and lambs. Monitoring changes in daily patterns across the annual production cycle while capturing changes in environmental conditions such as weather, day length, terrain and management could reveal key indicator metrics that may inform production and health and provide early warning systems for key issues in commercial flocks.Biotechnology & Biological Sciences Research Council (BBSRC

Effects of winter-feeding on reindeer’s future ability to utilize natural pastures

Winter feeding of reindeer (Rangifer tarandus tarandus) has become an increasingly common management action in reindeer husbandry in Sweden, Finland, and Norway when natural grazing resources are unavailable due to the loss of grazing grounds, disturbances, and icing events. In the short term, feeding increases survival and reproduction, but the long-term effects on reindeer’s ability to utilize natural pastures have not been investigated. Herders have raised concerns that fed reindeer, especially calves, do not utilize natural pastures as efficiently as other reindeer. In this thesis, I investigated the short- and long-term effects of winter feeding on reindeer with focus on habitat selection and future foraging behaviour. Interviews were conducted to collect experience-based knowledge on the effects of feeding among reindeer herders. An experimental study was conducted to test how winter feeding of calves during their first winter affects future habitat selection, foraging behaviour, and body weight. I found that there are several unintended effects of feeding that may compromise reindeer’s ability to use the natural pastures efficiently. In the interviews, the effects identified by herders were related to physical traits or behaviour; the reported effects varied between herders, as did the perception of whether an effect was positive or negative. In the experimental study, I found that reindeer calves which were fed in enclosures during their first winter of life were less likely to select areas with higher lichen abundance when on natural pasture compared to reindeer that had spent their first winter on natural pasture. Although, the control animals were also provided feed on pasture to some extent their first winter. Understanding the long-term impacts of winter feeding on reindeer and their ability to utilize natural pastures and adapt to changes in the environment may be crucial when evaluating the effects of different external forces on reindeer husbandry. Knowledge of the short- and long-term effects of feeding on reindeer is important for herders when evaluating if, when and how to feed their reindeer

Deep learning based classification of sheep behaviour from accelerometer data with imbalance

Classification of sheep behaviour from a sequence of tri-axial accelerometer data has the potential to enhance sheep management. Sheep behaviour is inherently imbalanced (e.g., more ruminating than walking) resulting in underperforming classification for the minority activities which hold importance. Existing works have not addressed class imbalance and use traditional machine learning techniques, e.g., Random Forest (RF). We investigated Deep Learning (DL) models, namely, Long Short Term Memory (LSTM) and Bidirectional LSTM (BLSTM), appropriate for sequential data, from imbalanced data. Two data sets were collected in normal grazing conditions using jaw-mounted and ear-mounted sensors. Novel to this study, alongside typical single classes, e.g., walking, depending on the behaviours, data samples were labelled with compound classes, e.g., walking_grazing. The number of steps a sheep performed in the observed 10 s time window was also recorded and incorporated in the models. We designed several multi-class classification studies with imbalance being addressed using synthetic data. DL models achieved superior performance to traditional ML models, especially with augmented data (e.g., 4-Class + Steps: LSTM 88.0%, RF 82.5%). DL methods showed superior generalisability on unseen sheep (i.e., F1-score: BLSTM 0.84, LSTM 0.83, RF 0.65). LSTM, BLSTM and RF achieved sub-millisecond average inference time, making them suitable for real-time applications. The results demonstrate the effectiveness of DL models for sheep behaviour classification in grazing conditions. The results also demonstrate the DL techniques can generalise across different sheep. The study presents a strong foundation of the development of such models for real-time animal monitoring